I raised this issue with the Tajik Ambassador in London last Friday. He called the MFA first thing this morning (Monday) to find it what is going on. They have said it is a computer error and they are updating the software to fix it. Those who received an overstay notification in error will get an update email shortly.

Has anyone had success in getting a follow-up to "clear" their status?

I received my third overstay penalty email today. The first two (using Google Translate) just said that my visa was expiring soon, but the one today said that I had overstayed and needed to go to the nearest embassy/consulate to pay a fine (original text below). I left Tajikistan via Kyzyl Art on 11 October last year. Contacted the embassy in the US twice with no response.